Kelly once tried to seduce Sean even though she knew he was gay. When he defended himself against her physical advances, he ended up giving her a bruise. Kelly was angry at him and cost him his job by claiming the bruise was from some kind of assault. Sean later got his job back and forgave Kelly. Despite these events, Kelly and Sean remained friends.

In 2006, Sean reunited with his 'father' Brian Tully, who had left his mother for another woman when Sean was ten. On Father's Day 2006, Brian revealed that he was not Sean's biological father, and that Sean's mother had in fact been having an affair with another man - a plumber called Paul Jones - who does not know that Sean exists.

Sean was involved in a storyline with Violet Wilson and Jamie Baldwin, when Violet became convinced that Jamie was in love with Sean, only to find that Jamie was actually in love with his step-mum, Frankie Baldwin.

In February 2007, Michelle Connor introduced Sean to her new boyfriend, Sonny Dhillon. Sean recognised Sonny as a former boyfriend. Sean confronted Sonny about their past relationship. Later, they rekindled their affair, but were soon discovered by both Jamie Baldwin and Steve McDonald. Michelle's brothers, Liam and Paul, questioned Sean about Steve's claims and later forced him to admit the truth to Michelle, devastingly ending her betrothal to Sonny.

In June 2007, Sean decided to be a sperm donor to Violet. After visiting the hospital with Violet for her twelve-week scan, Sean got the number of the sonographer, Marcus Dent, and started a romance with him. They went through a rough patch when Sean tricked his boyfriend into revealing the sex of the baby, totally disrespecting Violet as she didn't want to know whilst Sean did. It was revealed that Violet was expecting a boy. Sean and Violet fell out due to the fact that Sean wanted to be the baby's father but Violet saw him as the sperm donor as they had originally agreed. Sean looked into legal advice about the situation but it was too expensive. He and Violet finally called a truce and Sean lent Violet and Jamie the money for a flat together. Unfortunately Violet and Jamie found Sean's attention suffocating and agreed to move down to London together for a fresh start as a family. However, Violet went into labour at the Rovers Return on 22nd February, whilst Jamie was moving their things down to London, so Sean had to stay for the birth of his son. When he was born, Sean shouted out that he was the first person his son had seen. He was then seen bonding with his son whilst Violet was in hospital, upsetting Jamie who planned to be his father.

On 29th February, Jamie, Violet and Dylan left the Street but Violet's sister, Lauren, told Sean that they were leaving. Sean refused to believe that they were leaving forever and later blamed himself. Eventually he had tp admit they had gone for good. When Sean was jealous of Marcus staying with an ex in London, it became clear that it was time to move on. On 3rd September2008, at a party at Liam's, Sean fell for Tom Kerrigan. Sean asked Tom if he minded if he kissed him, Tom declined and Sean stormed off. Nevertheless, Sean and Marcus split a couple of days later.

In July 2009 Sean fell for a gay man named Leon whilst attending Weatherfield Health & Fitness with Jason. Trying to impress Leon, Sean claimed that Jason was his boyfriend, and during a later session at the gym, feigned being upset claiming that Jason had "dumped" him in order to invoke sympathy. This backfired however, when Leon stated he wasn't interested in camp men, and later admitted to Sean that he was in love with Jason. Sean tried to tell Leon that Jason wasn't gay, but he refused to believe him. After Jason won Mr Gay Weatherfield while drunk, the pair were forced to admit to Leon that Jason was straight. A shocked Leon then reported Jason and had him disqualified from the competition.

Sean decided to track down Dylan in 2010, but worried that Violet would turn him away, sent a friend request on Facescene posing as Liz McDonald, although initially angry, Liz became sympathetic as Sean only wanted to find his son, so she contacted Violet who then sent Sean a request on his own account as well as photographs of a two-year old Dylan.

Sean began visiting Dylan and Violet in London. On one visit on Easter Sunday in 2011, Sean was surprised to find Marcus at Violet and Jamie's residence. As Marcus and Violet were both going through relationship troubles, the two men took Dylan out for the day, but upon returning saw Jamie departing in a cab, seemingly ending their relationship. A sympathetic Sean offered to look after Dylan for a while but Violet accused him of trying to steal her son, and told him that the Violet he once knew was now gone. Sean retaliated by accusing Violet of being homophobic and not wanting to pollute Dylan with his mannerisms. He subsequently left and returned home.

Marcus later returned to Weatherfield and Sean reconciled their relationship. Over the summer they took care of Dylan after Violet ended up in hospital. In late 2012, the relationship ended after Marcus discovered he had feelings for Maria Connor and got together with her, which left Sean single once again.

The character of Sean Tully was introduced for a one-off basis in July 2003. Ten months later he appeared for a further two episodes in April 2004, before returning as a regular character four months later from August onward.